Same problem with my R5 II, RF 100-500 and RF 200-800 are all over the place since 1.0.3 firmware update.
If I pull the 200-800 in to about 600 it may take some sharper shots but it's very hit and miss.
The camera seems to be tracking BIF OK but it's not actually focussing on them. Birds sitting in reeds or trees seems to throw up the same problem, the camera recognises the subject but doesn't focus...
I held off doing the update for weeks to see if there were any problems being noted but after not seeing any I went for it, unfortunately what was a totally reliable camera before the update is now so hit and miss I have gone back to my R5 I until hopefully Canon sort this with another update to fix the issue.
As a side note, the problem doesn't seem to happen when using my old EF 500mm IS L II with the adapter ring...